Humanize skill

Humanize Skill

This skill only removes AI patterns; it does not perform general copy-editing, evaluate scientific quality, check journal formatting, or translate.

Read ${CLAUDE_SKILL_DIR}/references/ai_patterns.md at the start of every session, before scanning: the definitions, watch words, examples, detection greps, per-pattern fixes and the section-by-section priorities for all 27 patterns live only there.

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Workflow

Phase 1: Scan

Scan the section(s) the user provides for all 27 patterns. For response-to-reviewers letters and cover letters, prioritise Patterns 22-24. For a full manuscript, follow the per-section priorities in ai_patterns.md (Section-Specific Application Guide). For each pattern found, record its number and name, the count, the exact passage, and its location (paragraph number or line range).

Output: Pattern Frequency Table

## AI Pattern Scan Report

Section: {section name}
Word count: {N}

| # | Pattern | Count | Severity | Example from text |
|---|---------|-------|----------|-------------------|
| 1 | Significance inflation | 3 | HIGH | "...pivotal role in diagnostic imaging..." |
| ... | ... | ... | ... | ... |

Patterns not detected: 2, 4, 9, 14, 15

Total AI pattern instances: {N}
AI pattern density: {N per 1000 words}

Phase 2: Report

• Severity per pattern: HIGH (>3 occurrences), MEDIUM (1-3), LOW (0, clean).
• Density: total instances across all 27 patterns per 1000 words. Target: < 2.0.

Gate: Present the report and ask the user which patterns to fix. Default: fix all HIGH and MEDIUM.

Phase 3: Fix

Rewrite flagged passages with each pattern's fix from ai_patterns.md, under these rules:

1. Preserve technical accuracy. Every number, statistic, p-value, confidence interval, and clinical fact must remain identical.
2. Preserve citations. Never add, remove, or relocate a citation.
3. Keep the formal academic register of an experienced radiologist writing for peers in a top-tier journal. Never make the text casual or conversational.
4. Keep domain-specific terminology intact. "Convolutional neural network," "apparent diffusion coefficient," "Fleiss' kappa" stay as-is.
5. Never introduce new claims, remove existing ones, or change a sentence's meaning — rephrase, never reinterpret. If a passage cannot be fixed without changing its meaning, leave it and flag it for the user.
6. Use active voice where natural: "We analyzed" rather than "Analysis was performed."
7. Vary sentence structure. Mix short declarative sentences (8-12 words) with longer ones (25-35 words). A de-AI pass tends to flatten rhythm — it shortens the long sentences and pads the short ones toward a comfortable middle, which is itself a tell. scripts/check_sentence_variety.py verifies this rule in Phase 4.
8. Thin out antithesis and cleft constructions (Pattern 27, the M2 heuristic). For each "X rather than Y", "not X but Y" or "X, not Y", apply the negative-form test: delete the negative half and rewrite the clause in the positive. If a fact disappears, the contrast was functional — keep it; if nothing disappears, it was decoration — cut it. Judge by the manuscript's overall rate, not instance by instance, and keep two or three for emphasis. Rewrite clefts ("What … is …", "It is … that …") in plain subject-verb order ("What matters is X" → "X matters"). scripts/check_rhetorical_density.py (in /self-review) measures this in Phase 4.

Output: Present the rewritten text with changes highlighted using diff format or tracked changes.

Phase 4: Verify

Keep the pre-rewrite text. Before editing in place, copy the original somewhere the fidelity check can read it (cp manuscript.md /tmp/pre_humanize.md). Without it Phase 4 can only re-scan for patterns — it cannot tell whether the rewrite preserved numbers and citations.

Run both deterministic checks, then re-scan the rewritten text using the same 27 patterns.

python3 "${CLAUDE_SKILL_DIR}/scripts/check_rewrite_fidelity.py" \
    --before /tmp/pre_humanize.md --after manuscript.md \
    --out qc/rewrite_fidelity.json --strict
python3 "${CLAUDE_SKILL_DIR}/scripts/check_sentence_variety.py" \
    --manuscript manuscript.md --out qc/sentence_variety.json

NUMBER_DRIFT, NUMBER_REASSIGNED, CITATION_DROP or CITATION_MOVED means the rewrite broke an invariant — revert that passage, redo it, and flag it for the user. EDIT_FOOTPRINT_HIGH is advisory: Patterns 6 and 18 replace whole paragraphs by design, so a correct pass over an inflated draft can exceed 60% of words changed. Read the diff and confirm the author's argument survived rather than assuming the percentage is a defect.

Known limits: the fidelity gate does not check an added or removed negation, a number written in words, a changed unit, or a direction word next to a non-percentage. A clean exit does not clear these; read the diff for them.

Output: Verification Report

## Verification Report

| Metric | Before | After |
|--------|--------|-------|
| Total instances | 23 | 4 |
| Density (per 1000 words) | 8.2 | 1.4 |
| HIGH severity patterns | 3 | 0 |
| MEDIUM severity patterns | 5 | 2 |

Remaining issues:
- Pattern 17 (hedging): 2 instances remain -- appropriate for the evidence level.

Verdict: PASS (density < 2.0)

If the density remains above 2.0, run another fix-verify cycle (max 3 rounds). When called by another skill, return the verification report so the calling skill can check the pass/fail status.

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The 27 Detection Patterns

All 27 are defined in references/ai_patterns.md. Two carry rules to apply exactly as written:

#	Pattern	What to look for	Fix
13	Em dash overuse	More than 2 em dashes per 1000 words (the /self-review classical-style gate fails a manuscript above 25 prose em-dashes)	Use parentheses or restructure. After converting — X — appositives to (X), run the paren-span safety scan (python3 "${CLAUDE_SKILL_DIR}/../self-review/scripts/check_paren_spans.py"): a bulk conversion can pair two unrelated dashes across a sentence boundary and wrap a whole sentence (or an ordinal "Sixth, …" limitation) inside one parenthesis — paren-balanced but broken, so a balance check misses it. Operate per-sentence; never match across .
21	AI Disclosure boilerplate (body)	"## Artificial Intelligence Disclosure", "Generative AI was not used to create..." in manuscript body	Put it where the target journal asks (the journal profile's Disclosure location): Methods or Acknowledgments for some journals, cover letter, title page or submission form only for others. Do not delete a disclosure the journal requires in the body

Patterns 22-24 apply only to response-to-reviewers letters and editor cover letters, not manuscript bodies. They are defined once in ai_patterns.md (Response-Letter Patterns); for authoring guidance, see the revise skill's references/r2r_voice.md.

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Gates

Gate	Severity	Trigger	Action on fail
AI-pattern density target	ADVISORY	density > 2.0 patterns / 1000 words after sweep	warn; surface remaining flagged passages for manual review
Pattern 13 — paren-span corruption after em-dash conversion	ENFORCED	after a — X — → (X) sweep	run python3 "${CLAUDE_SKILL_DIR}/../self-review/scripts/check_paren_spans.py" --strict; PAREN_SPAN_ORDINAL / PAREN_SPAN_SENTENCE means a conversion wrapped a sentence/ordinal inside parens — fix before finalizing
Pattern 19 — § symbol	ENFORCED (senior MA reviewer prep)	grep -c "§" manuscript.md > 0	auto-strip; verify post-rewrite count == 0
Pattern 20 — (see Methods §X) self-reference	ENFORCED	match found	rewrite to direct section name reference
Pattern 21 — AI disclosure in the wrong place	ENFORCED	an AI-use disclosure in the body of a journal that wants it elsewhere, or repeated in several places	move it to where the target journal asks (journal profile); never reword a required disclosure to hide the tool
Pattern 26 — aphorism density	ENFORCED	negative-definition rate AND short-declarative share both over threshold	run python3 "${CLAUDE_SKILL_DIR}/../self-review/scripts/check_aphorism_density.py" --manuscript manuscript.md; APHORISM_DENSITY (Minor) means the prose is a run of epigrams with the explanatory sentences compressed out — absorb most of them into the neighbouring sentence and write the explanation back, keeping two or three for emphasis; do NOT simply delete them, which shortens the prose further
Pattern 27 — antithesis / cleft density	ENFORCED	"rather than" / "not X but Y" / "X, not Y" or "What … is …" / "It is … that …" over a per-1000 threshold AND raw-count floor	run python3 "${CLAUDE_SKILL_DIR}/../self-review/scripts/check_rhetorical_density.py" --manuscript manuscript.md; ANTITHESIS_DENSITY / CLEFT_DENSITY (both Minor) — apply Fix rule 8 (the M2 test). A lone functional "rather than" or "instead of" never fires
Pattern 25 — inline-emphasis over-use	ENFORCED	italic-emphasis density over threshold after allowlist	run python3 "${CLAUDE_SKILL_DIR}/../self-review/scripts/check_emphasis_density.py" --manuscript manuscript.md; EMPHASIS_OVERUSE (Minor) means strip inline italics (keep only stat symbols / Latin / gene-species); whole-clause italics are the strongest tell
Patterns 22-24 — R2R editing-mechanism / draft line-number / tooling leak	TRIAGE (response letters); § = 0 hard	detection greps in ai_patterns.md R2R section surface candidates	review each hit (analysis narration, quoted additions, revised-manuscript page/line are NOT tells); rewrite confirmed tells to substantive prose
Citation preservation invariant	ENFORCED	a citation item (each key of a multi-key or locator Pandoc citation, or a numeric marker) removed or changed, or moved out of the sentence of the word it was attached to while that word kept its place	scripts/check_rewrite_fidelity.py --before <pre> --after <post> --strict → CITATION_DROP / CITATION_MOVED (Major); revert that single rewrite and flag for the user
Numerical preservation invariant	ENFORCED	a numeric token's count changed (sign, inequality sign and %-direction are part of the token; writing a sign out in words also fires), or values traded places while the words around them stayed	same script → NUMBER_DRIFT / NUMBER_REASSIGNED (Major); revert and flag. Known limits: a negation, a number written in words, a unit, or a direction word next to a non-percentage is not checked — read the diff for these
Rewrite footprint	ADVISORY	fraction of word tokens changed exceeds --warn-pct (default 70)	EDIT_FOOTPRINT_HIGH (Minor) — never blocks; read the diff (Phase 4)
Fix rule 7 — sentence-length uniformity	ADVISORY	prose has no short (≤12 words) or no long (≥25 words) sentences	scripts/check_sentence_variety.py --manuscript <file> → SENTENCE_UNIFORM (Minor); break up or combine sentences until both bands exist. Silent below 15 sentences